Sonoita Creek is a stream in Santa Cruz County, Arizona. It originates near and takes its name from the abandoned Pima mission in the high valley near Sonoita. It flows steadily for the first fifteen miles (24 km) of its westward course past Patagonia, its bird sanctuary and Patagonia Lake, but sinks beneath the sand seven to eight miles (13 km) before joining the Santa Cruz River a few miles north of Nogales. This confluence provides water for Tumacácori and Tubac and collects in the marsh lands around San Xavier del Bac downstream, to the north. The Santa Rita Mountains lie to the north and the Canelo Hills, Red Mountain and the Patagonia Mountains lie to the south. Harshaw Creek is a southern tributary which joins the Sonoita near Patagonia. Harshaw Creek drains the area between the Patagonia Mountains to the west and the high San Raphael valley grasslands to the east. The old mining area and ghost towns of Harshaw, Mowry, Washington Camp, and Duquesne lie within its watershed.
On November 17, 1856, the United States Army established Fort Buchanan along its banks in an effort to control the newly acquired Gadsden Purchase.
In the 1890s several stone artifacts were discovered a few feet beneath the surface near the beginning of the river.
The New Mexico and Arizona Railroad paralleled the Sonoita Creek for a portion of the Railroad's route. The route ran from a connection with the Southern Pacific Railroad at Benson, Arizona, then south to Fairbank (about 13 km or 8 miles west of Tombstone, Arizona) then west to Sonoita - Patagonia and Calabassas (today known as Rio Rico, Arizona), then south to Nogales. The railroad was constructed 1881-1882 and was abandoned in 5 phases between 1927 - 1962. Only 15.74 km (9.78 mi) of track remains in place today, from Calabassas (Rio Rico) to Nogales and is operated by the Union Pacific Railroad.